Abstract Headaches (HA), muscle and joint pain and depression are some of the most common debilitating symptoms in military personnel served in the 1990-1991 Persian Gulf War (GW1). Migraine like HA and diffuse body pain were detected in 64% of Gulf War Veteran (GWV) diagnosed with Gulf War Veterans? Illnesses (GWVI). Likewise, depression carries a very high co- morbid prevalence (50%) in patients with chronic pain, and in GWV with GWVI related chronic HA, and body muscle and joint pain conditions (GWVI-HAP). Repetitive transcranial magnetic stimulation (rTMS) offers an effective non-invasive treatment option for GWVI-HAP. Our preliminary study funded by the DOD Innovation Treatment Evaluation Award for GWVI demonstrated that a short course (4 sessions) of rTMS at the motor cortex could significantly reduce GWI-HAP symptoms up to two months. This multi-center clinical trial study aims to further: 1) valid the long-term efficacy of the treatment for GWI-HAP and depression; and 2) assess site specificity of the treatment for both pain and depression. !